partis-bcr 1.0.11__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- bin/partis +1 -1
- bin/partis-test.py +6 -0
- bin/partis.py +1 -1
- {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
- {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +644 -126
- python/recombinator.py +2 -0
- python/treegenerator.py +1 -1
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
- test/new-results/annotate-new-simu.yaml +1 -0
- test/new-results/cache-new-partition.csv +59 -0
- test/new-results/get-selection-metrics-new-simu.yaml +1 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
- test/new-results/multi-annotate-new-simu.yaml +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
- test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
- test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
- test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
- test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
- test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
- test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
- test/new-results/partition-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
- test/new-results/partition-new-simu.yaml +1 -0
- test/new-results/run-times.csv +9 -0
- test/new-results/seed-partition-new-simu.yaml +1 -0
- test/new-results/test/parameters/data/hmm/all-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/hmm/all-mean-n-muted.csv +155 -0
- test/new-results/test/parameters/data/hmm/all-probs.csv +44 -0
- test/new-results/test/parameters/data/hmm/cluster_size.csv +2 -0
- test/new-results/test/parameters/data/hmm/d-mean-mute-freqs.csv +43 -0
- test/new-results/test/parameters/data/hmm/d-mean-n-muted.csv +14 -0
- test/new-results/test/parameters/data/hmm/d_gene-d_3p_del-probs.csv +34 -0
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+
IGHD2-21_star_02_2: 0.017857142857142856
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|
26
|
+
IGHD2-21_star_02_20: 0.017857142857142856
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|
27
|
+
IGHD2-21_star_02_21: 0.017857142857142856
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|
28
|
+
IGHD2-21_star_02_22: 0.017857142857142856
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|
29
|
+
IGHD2-21_star_02_23: 0.017857142857142856
|
|
30
|
+
IGHD2-21_star_02_24: 0.017857142857142856
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|
31
|
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IGHD2-21_star_02_25: 0.017857142857142856
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|
32
|
+
IGHD2-21_star_02_26: 0.017857142857142856
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|
33
|
+
IGHD2-21_star_02_27: 0.017857142857142856
|
|
34
|
+
IGHD2-21_star_02_3: 0.017857142857142856
|
|
35
|
+
IGHD2-21_star_02_4: 0.017857142857142856
|
|
36
|
+
IGHD2-21_star_02_5: 0.017857142857142856
|
|
37
|
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IGHD2-21_star_02_6: 0.017857142857142856
|
|
38
|
+
IGHD2-21_star_02_7: 0.017857142857142856
|
|
39
|
+
IGHD2-21_star_02_8: 0.017857142857142856
|
|
40
|
+
IGHD2-21_star_02_9: 0.017857142857142856
|
|
41
|
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insert_left_A: 0.09398496240601503
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|
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|
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insert_left_C: 0.16917293233082706
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|
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|
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insert_left_G: 0.11654135338345864
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|
44
|
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insert_left_T: 0.12030075187969924
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|
45
|
+
- !!python/object:python.hmmwriter.State
|
|
46
|
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emissions:
|
|
47
|
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probs:
|
|
48
|
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A: 0.8915122136693276
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|
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|
+
C: 0.03616259544355744
|
|
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|
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G: 0.03616259544355744
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|
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|
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T: 0.03616259544355744
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|
52
|
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track: nukes
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|
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|
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extras:
|
|
54
|
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ambiguous_char: N
|
|
55
|
+
ambiguous_emission_prob: 0.25
|
|
56
|
+
germline: A
|
|
57
|
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name: insert_left_A
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|
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transitions:
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59
|
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IGHD2-21_star_02_1: 0.017857142857142856
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61
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IGHD2-21_star_02_10: 0.017857142857142856
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62
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IGHD2-21_star_02_11: 0.017857142857142856
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63
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IGHD2-21_star_02_12: 0.017857142857142856
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64
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IGHD2-21_star_02_13: 0.017857142857142856
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65
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IGHD2-21_star_02_14: 0.017857142857142856
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66
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IGHD2-21_star_02_15: 0.017857142857142856
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|
67
|
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IGHD2-21_star_02_16: 0.017857142857142856
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|
68
|
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IGHD2-21_star_02_17: 0.017857142857142856
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|
69
|
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IGHD2-21_star_02_18: 0.017857142857142856
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|
70
|
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IGHD2-21_star_02_19: 0.017857142857142856
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71
|
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IGHD2-21_star_02_2: 0.017857142857142856
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72
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IGHD2-21_star_02_20: 0.017857142857142856
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73
|
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IGHD2-21_star_02_21: 0.017857142857142856
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74
|
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IGHD2-21_star_02_22: 0.017857142857142856
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|
75
|
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IGHD2-21_star_02_23: 0.017857142857142856
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76
|
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IGHD2-21_star_02_24: 0.017857142857142856
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77
|
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IGHD2-21_star_02_25: 0.017857142857142856
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|
78
|
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IGHD2-21_star_02_26: 0.017857142857142856
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|
79
|
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IGHD2-21_star_02_27: 0.017857142857142856
|
|
80
|
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IGHD2-21_star_02_3: 0.017857142857142856
|
|
81
|
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IGHD2-21_star_02_4: 0.017857142857142856
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|
82
|
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IGHD2-21_star_02_5: 0.017857142857142856
|
|
83
|
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IGHD2-21_star_02_6: 0.017857142857142856
|
|
84
|
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IGHD2-21_star_02_7: 0.017857142857142856
|
|
85
|
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IGHD2-21_star_02_8: 0.017857142857142856
|
|
86
|
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IGHD2-21_star_02_9: 0.017857142857142856
|
|
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|
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insert_left_A: 0.09398496240601503
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|
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|
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insert_left_C: 0.16917293233082706
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|
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|
+
insert_left_G: 0.11654135338345864
|
|
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|
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insert_left_T: 0.12030075187969924
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|
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|
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- !!python/object:python.hmmwriter.State
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|
92
|
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emissions:
|
|
93
|
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probs:
|
|
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|
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A: 0.03616259544355744
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|
95
|
+
C: 0.8915122136693276
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|
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|
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G: 0.03616259544355744
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|
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T: 0.03616259544355744
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|
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|
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track: nukes
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|
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|
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extras:
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100
|
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ambiguous_char: N
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|
101
|
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ambiguous_emission_prob: 0.25
|
|
102
|
+
germline: C
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|
103
|
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name: insert_left_C
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|
104
|
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transitions:
|
|
105
|
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IGHD2-21_star_02_0: 0.017857142857142856
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|
106
|
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IGHD2-21_star_02_1: 0.017857142857142856
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|
107
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IGHD2-21_star_02_10: 0.017857142857142856
|
|
108
|
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IGHD2-21_star_02_11: 0.017857142857142856
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|
109
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IGHD2-21_star_02_12: 0.017857142857142856
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|
110
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IGHD2-21_star_02_13: 0.017857142857142856
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|
111
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IGHD2-21_star_02_14: 0.017857142857142856
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|
112
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IGHD2-21_star_02_15: 0.017857142857142856
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|
113
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IGHD2-21_star_02_16: 0.017857142857142856
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|
114
|
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IGHD2-21_star_02_17: 0.017857142857142856
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|
115
|
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IGHD2-21_star_02_18: 0.017857142857142856
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116
|
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IGHD2-21_star_02_19: 0.017857142857142856
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|
117
|
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IGHD2-21_star_02_2: 0.017857142857142856
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118
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IGHD2-21_star_02_20: 0.017857142857142856
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119
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IGHD2-21_star_02_21: 0.017857142857142856
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120
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IGHD2-21_star_02_22: 0.017857142857142856
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121
|
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IGHD2-21_star_02_23: 0.017857142857142856
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122
|
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IGHD2-21_star_02_24: 0.017857142857142856
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|
123
|
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IGHD2-21_star_02_25: 0.017857142857142856
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|
124
|
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IGHD2-21_star_02_26: 0.017857142857142856
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|
125
|
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IGHD2-21_star_02_27: 0.017857142857142856
|
|
126
|
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IGHD2-21_star_02_3: 0.017857142857142856
|
|
127
|
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IGHD2-21_star_02_4: 0.017857142857142856
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|
128
|
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IGHD2-21_star_02_5: 0.017857142857142856
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|
129
|
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IGHD2-21_star_02_6: 0.017857142857142856
|
|
130
|
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IGHD2-21_star_02_7: 0.017857142857142856
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|
131
|
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IGHD2-21_star_02_8: 0.017857142857142856
|
|
132
|
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IGHD2-21_star_02_9: 0.017857142857142856
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|
133
|
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insert_left_A: 0.09398496240601503
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|
134
|
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insert_left_C: 0.16917293233082706
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|
135
|
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insert_left_G: 0.11654135338345864
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|
136
|
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insert_left_T: 0.12030075187969924
|
|
137
|
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- !!python/object:python.hmmwriter.State
|
|
138
|
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emissions:
|
|
139
|
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probs:
|
|
140
|
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A: 0.03616259544355744
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|
141
|
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C: 0.03616259544355744
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|
142
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G: 0.8915122136693276
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|
143
|
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T: 0.03616259544355744
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|
144
|
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track: nukes
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|
145
|
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extras:
|
|
146
|
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ambiguous_char: N
|
|
147
|
+
ambiguous_emission_prob: 0.25
|
|
148
|
+
germline: G
|
|
149
|
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name: insert_left_G
|
|
150
|
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transitions:
|
|
151
|
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IGHD2-21_star_02_0: 0.017857142857142856
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|
152
|
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IGHD2-21_star_02_1: 0.017857142857142856
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|
153
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IGHD2-21_star_02_10: 0.017857142857142856
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|
154
|
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IGHD2-21_star_02_11: 0.017857142857142856
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|
155
|
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IGHD2-21_star_02_12: 0.017857142857142856
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|
156
|
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IGHD2-21_star_02_13: 0.017857142857142856
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|
157
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IGHD2-21_star_02_14: 0.017857142857142856
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|
158
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IGHD2-21_star_02_15: 0.017857142857142856
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|
159
|
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IGHD2-21_star_02_16: 0.017857142857142856
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|
160
|
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IGHD2-21_star_02_17: 0.017857142857142856
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|
161
|
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IGHD2-21_star_02_18: 0.017857142857142856
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|
162
|
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IGHD2-21_star_02_19: 0.017857142857142856
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|
163
|
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IGHD2-21_star_02_2: 0.017857142857142856
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164
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IGHD2-21_star_02_20: 0.017857142857142856
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165
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IGHD2-21_star_02_21: 0.017857142857142856
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|
166
|
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IGHD2-21_star_02_22: 0.017857142857142856
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|
167
|
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IGHD2-21_star_02_23: 0.017857142857142856
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|
168
|
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IGHD2-21_star_02_24: 0.017857142857142856
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|
169
|
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IGHD2-21_star_02_25: 0.017857142857142856
|
|
170
|
+
IGHD2-21_star_02_26: 0.017857142857142856
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|
171
|
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IGHD2-21_star_02_27: 0.017857142857142856
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|
172
|
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IGHD2-21_star_02_3: 0.017857142857142856
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|
173
|
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IGHD2-21_star_02_4: 0.017857142857142856
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|
174
|
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IGHD2-21_star_02_5: 0.017857142857142856
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|
175
|
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IGHD2-21_star_02_6: 0.017857142857142856
|
|
176
|
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IGHD2-21_star_02_7: 0.017857142857142856
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|
177
|
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IGHD2-21_star_02_8: 0.017857142857142856
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|
178
|
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IGHD2-21_star_02_9: 0.017857142857142856
|
|
179
|
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insert_left_A: 0.09398496240601503
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|
180
|
+
insert_left_C: 0.16917293233082706
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|
181
|
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insert_left_G: 0.11654135338345864
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|
182
|
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insert_left_T: 0.12030075187969924
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|
183
|
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- !!python/object:python.hmmwriter.State
|
|
184
|
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emissions:
|
|
185
|
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probs:
|
|
186
|
+
A: 0.03616259544355744
|
|
187
|
+
C: 0.03616259544355744
|
|
188
|
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G: 0.03616259544355744
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|
189
|
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T: 0.8915122136693276
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|
190
|
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track: nukes
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|
191
|
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extras:
|
|
192
|
+
ambiguous_char: N
|
|
193
|
+
ambiguous_emission_prob: 0.25
|
|
194
|
+
germline: T
|
|
195
|
+
name: insert_left_T
|
|
196
|
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transitions:
|
|
197
|
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IGHD2-21_star_02_0: 0.017857142857142856
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|
198
|
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IGHD2-21_star_02_1: 0.017857142857142856
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|
199
|
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IGHD2-21_star_02_10: 0.017857142857142856
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|
200
|
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IGHD2-21_star_02_11: 0.017857142857142856
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|
201
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IGHD2-21_star_02_12: 0.017857142857142856
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|
202
|
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IGHD2-21_star_02_13: 0.017857142857142856
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|
203
|
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IGHD2-21_star_02_14: 0.017857142857142856
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|
204
|
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IGHD2-21_star_02_15: 0.017857142857142856
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|
205
|
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IGHD2-21_star_02_16: 0.017857142857142856
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|
206
|
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IGHD2-21_star_02_17: 0.017857142857142856
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|
207
|
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IGHD2-21_star_02_18: 0.017857142857142856
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|
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IGHD2-21_star_02_19: 0.017857142857142856
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|
209
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IGHD2-21_star_02_2: 0.017857142857142856
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210
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IGHD2-21_star_02_20: 0.017857142857142856
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IGHD2-21_star_02_21: 0.017857142857142856
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IGHD2-21_star_02_22: 0.017857142857142856
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|
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IGHD2-21_star_02_23: 0.017857142857142856
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|
214
|
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IGHD2-21_star_02_24: 0.017857142857142856
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|
215
|
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IGHD2-21_star_02_25: 0.017857142857142856
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|
216
|
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IGHD2-21_star_02_26: 0.017857142857142856
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|
217
|
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IGHD2-21_star_02_27: 0.017857142857142856
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|
218
|
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IGHD2-21_star_02_3: 0.017857142857142856
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|
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|
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IGHD2-21_star_02_4: 0.017857142857142856
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|
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IGHD2-21_star_02_5: 0.017857142857142856
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|
221
|
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IGHD2-21_star_02_6: 0.017857142857142856
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|
222
|
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IGHD2-21_star_02_7: 0.017857142857142856
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|
223
|
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IGHD2-21_star_02_8: 0.017857142857142856
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|
224
|
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IGHD2-21_star_02_9: 0.017857142857142856
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|
225
|
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insert_left_A: 0.09398496240601503
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|
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|
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insert_left_C: 0.16917293233082706
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|
227
|
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insert_left_G: 0.11654135338345864
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|
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|
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insert_left_T: 0.12030075187969924
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|
229
|
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- !!python/object:python.hmmwriter.State
|
|
230
|
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emissions:
|
|
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|
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probs:
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|
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|
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A: 0.8915122136693276
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|
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|
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C: 0.03616259544355744
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|
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|
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G: 0.03616259544355744
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|
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|
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T: 0.03616259544355744
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|
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|
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track: nukes
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|
237
|
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extras:
|
|
238
|
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ambiguous_char: N
|
|
239
|
+
ambiguous_emission_prob: 0.25
|
|
240
|
+
germline: A
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|
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|
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name: IGHD2-21_star_02_0
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|
242
|
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transitions:
|
|
243
|
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IGHD2-21_star_02_1: 0.9642857142857143
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|
244
|
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end: 0.03571428571428571
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|
245
|
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- !!python/object:python.hmmwriter.State
|
|
246
|
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emissions:
|
|
247
|
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probs:
|
|
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|
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A: 0.03613029098567235
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|
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|
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C: 0.03613029098567235
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|
250
|
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G: 0.8916091270429829
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|
251
|
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T: 0.03613029098567235
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|
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|
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track: nukes
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|
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|
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extras:
|
|
254
|
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ambiguous_char: N
|
|
255
|
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ambiguous_emission_prob: 0.25
|
|
256
|
+
germline: G
|
|
257
|
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name: IGHD2-21_star_02_1
|
|
258
|
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transitions:
|
|
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|
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IGHD2-21_star_02_2: 0.9642857142857143
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|
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|
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end: 0.03571428571428571
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|
261
|
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- !!python/object:python.hmmwriter.State
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|
262
|
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emissions:
|
|
263
|
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probs:
|
|
264
|
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A: 0.036097986527787264
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|
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C: 0.8917060404166381
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|
266
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G: 0.036097986527787264
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|
267
|
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T: 0.036097986527787264
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|
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track: nukes
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|
269
|
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extras:
|
|
270
|
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ambiguous_char: N
|
|
271
|
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ambiguous_emission_prob: 0.25
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|
272
|
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germline: C
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|
273
|
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name: IGHD2-21_star_02_2
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|
274
|
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transitions:
|
|
275
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595
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IGHD2-21_star_02_23: 0.9642857142857143
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596
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597
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- !!python/object:python.hmmwriter.State
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|
598
|
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|
599
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|
600
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601
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603
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605
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|
606
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|
607
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|
608
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germline: A
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|
609
|
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|
610
|
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|
611
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|
612
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end: 0.03571428571428571
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|
613
|
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- !!python/object:python.hmmwriter.State
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|
614
|
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|
615
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|
616
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|
617
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|
618
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G: 0.03606568206990218
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|
619
|
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|
620
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track: nukes
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|
621
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|
622
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ambiguous_char: N
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|
623
|
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ambiguous_emission_prob: 0.25
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|
624
|
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germline: T
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|
625
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|
626
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|
627
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|
628
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|
629
|
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- !!python/object:python.hmmwriter.State
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|
630
|
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|
|
631
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|
632
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|
633
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|
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G: 0.036097986527787264
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|
635
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|
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|
638
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|
639
|
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|
640
|
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germline: T
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|
641
|
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name: IGHD2-21_star_02_25
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|
642
|
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644
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|
645
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|
646
|
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|
647
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|
648
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|
649
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650
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G: 0.03631119594982884
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651
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T: 0.03631119594982884
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652
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653
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extras:
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|
654
|
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ambiguous_char: N
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|
655
|
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ambiguous_emission_prob: 0.25
|
|
656
|
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germline: C
|
|
657
|
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name: IGHD2-21_star_02_26
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|
658
|
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transitions:
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|
659
|
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IGHD2-21_star_02_27: 0.9642857142857143
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|
660
|
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end: 0.03571428571428571
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|
661
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- !!python/object:python.hmmwriter.State
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|
662
|
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emissions:
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|
663
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probs:
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|
664
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|
665
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|
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G: 0.03616259544355744
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667
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|
668
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track: nukes
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|
669
|
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|
670
|
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ambiguous_char: N
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|
671
|
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ambiguous_emission_prob: 0.25
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|
672
|
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germline: C
|
|
673
|
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name: IGHD2-21_star_02_27
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|
674
|
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transitions:
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|
675
|
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end: 1.0
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|
676
|
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tracks:
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677
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nukes:
|
|
678
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- A
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|
679
|
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- C
|
|
680
|
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- G
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|
681
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- T
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